* using log directory 'd:/RCompile/CRANincoming/R-devel/Seurat.Rcheck' * using R Under development (unstable) (2025-01-07 r87537 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'Seurat/DESCRIPTION' ... OK * this is package 'Seurat' version '5.2.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [30s] INFO Maintainer: 'Rahul Satija ' Suggests or Enhances not in mainstream repositories: BPCells, enrichR, presto Availability using Additional_repositories specification: BPCells yes https://bnprks.r-universe.dev enrichR yes https://satijalab.r-universe.dev presto yes https://satijalab.r-universe.dev * checking package namespace information ... OK * checking package dependencies ... INFO Packages suggested but not available for checking: 'BPCells', 'presto' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'Seurat' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * used C++ compiler: 'g++.exe (GCC) 13.3.0' * checking C++ specification ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Error: there is no package called 'ggplot2' Call sequence: 9: doWithOneRestart(return(expr), restart) 8: withOneRestart(expr, restarts[[1L]]) 7: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted * checking S3 generic/method consistency ... WARNING Error: there is no package called 'ggplot2' Call sequence: 9: doWithOneRestart(return(expr), restart) 8: withOneRestart(expr, restarts[[1L]]) 7: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted See section 'Generic functions and methods' in the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: there is no package called 'ggplot2' Call sequence: 9: doWithOneRestart(return(expr), restart) 8: withOneRestart(expr, restarts[[1L]]) 7: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted The argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... NOTE Error: there is no package called 'ggplot2' Call sequence: 9: doWithOneRestart(return(expr), restart) 8: withOneRestart(expr, restarts[[1L]]) 7: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... [33s] NOTE Error: there is no package called 'scattermore' Call sequence: 7: doWithOneRestart(return(expr), restart) 6: withOneRestart(expr, restarts[[1L]]) 5: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'ggplot2' Calls: Execution halted Error: there is no package called 'scattermore' Call sequence: 7: doWithOneRestart(return(expr), restart) 6: withOneRestart(expr, restarts[[1L]]) 5: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted * checking Rd files ... [13s] WARNING IntegrateLayers.Rd:44: there is no package called 'sctransform' problem found in 'IntegrateLayers.Rd' * checking Rd metadata ... OK * checking Rd line widths ... NOTE Error: IntegrateLayers.Rd:44: there is no package called 'sctransform' Execution halted These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [59s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [240s] OK Running 'testthat.R' [240s] * checking PDF version of manual ... [43s] OK * checking HTML version of manual ... [60s] OK * DONE Status: 3 WARNINGs, 4 NOTEs